Question: a question about copy number alterations
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8 months ago by
15617759110
15617759110 wrote:

enter image description here

this table is the supplementary table 9 of Copy number alterations across all tumors supplenmented in paper'Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors'. From line 2 to 169(the image just show part of that) ,the sample ID is AC-DFCI_AC_PD1-1-TP-NT-SM-9LRI9-SM-9LRIA which corresponds to patient ID AC_PD1-1(which is shown in the clinical data,not shown here). What I want to get from this table is the total CNAs of one patient and how could I realize that? Some may say that it is a 'segment' file and you can do it as the common pipeline shows.But I noticed that it supplied the 'corrected_total_cn' of each sample.Does this mean that I can directly sum the corrected_total_cn of the same sample ID and then get the total CNA of one corresponding patient?

Here is the url https://www.nature.com/articles/s41588-018-0200-2#Sec24 of supplement materials and methods

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